cleanCrystal.rb

This makes POSCAR fit appropriate structure when POSCAR is distorted from the expected symmetrical structure. Usually this reads syminfo.yaml and knows axis, atomic positions and symmetry operations. Instead of the cell information containing in syminfo.yaml, POSCAR file can be read using poscar option. Cell parameters are not treated by symmetry and must be fit by hand.

usage

	cleanCrystal.rb [OPTION] [syminfo.yaml]

option

--bravais, -b

Cell parameters are made fit to Bravais lattice. ``auto'', ``cubic'', ``tetra'', ``ortho'', ``rhombo'' and ``other'' can be set. This is runaround implementation.

default = other

--center, -c

Specified atom is sent to position specified by --shift.

--decimal, -d

Cutoff decimals

default = 1e-16

--poscar

Cell information is read from POSCAR style file.

--shift, -s

Atominc positoin is set to this value. It is required to be used with --center option.

default = ``0 0 0''

--swap

Swap axes. ``ab'', ``bc'' and ``ca'' are supported.

default = false

--symprec

Symmetry check tolerance in reduced coordinate

default = 1e-2

example

	cleanCrystal.rb -c 1 -s "0.5 0.5 0" -b auto --swap=ab